Hi all,
My galaxy is the last update and I work with samtools 1.2. I have a bug with the sorting and the upload of bam file. This bug appears only when I try to upload bam sorted by name or when I try to sort by name. When I work with bam sorted by coordinate, there is no problem.
So, when I try to sort a bam file by name, this error appears under the "bug icon" :
Tool execution generated the following error message: [bam_sort_core] merging from 20 files... *** Error in `python': double free or corruption (!prev): 0x0000000002897990 *** Aborted (core dumped)
The tool produced the following additional output:
[E::hts_idx_push] chromosome blocks not continuous Galaxy attempted to build the BAM index with samtools 1.0+ but failed: [Errno 2] No such file or directory: '/data/galaxy-dist/database/job_working_directory/024/24109/__dataset_48619_metadata_temp_file_MqhjBN.bai'
And the same type of error appears when I try to upload bam sorted by name.
What I understand is that the bam can be sorted properly (The command line to sort is ok in a terminal with no bug and I can follow this step in the job_working_directory during the run) but Galaxy seems to fail to create a bai.
For our analysis pipeline, I think the bai is not crucial, is it possible to avoid this creation of bai during uploading and sorting of bam file by name ?
Is there another problem than this creation of bai ?
Thanks.
Julie